BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818918.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,915,031 number of mapped reads = 1,891,743 (98.78%) number of supplementary alignments = 26,362 (1.38%) number of secondary alignments = 0 number of mapped bases = 175,382,391 bp number of sequenced bases = 175,267,471 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 452,856 duplication rate = 20.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2145 >>>>>>> ACTG content number of A's = 49,704,725 bp (28.36%) number of C's = 37,087,898 bp (21.16%) number of T's = 50,169,247 bp (28.62%) number of G's = 38,302,909 bp (21.85%) number of N's = 2,692 bp (0%) GC percentage = 43.01% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,062,757 number of insertions = 25,492 mapped reads with insertion percentage = 1.3% number of deletions = 58,391 mapped reads with deletion percentage = 3.01% homopolymer indels = 39.87% >>>>>>> Coverage mean coverageData = 0.0567X std coverageData = 0.728X There is a 3.81% of reference with a coverageData >= 1X There is a 1.07% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 16315984 0.06546015385855347 1.0031931820658835 chr2 243199373 13147765 0.05406167309485621 1.1130200218953716 chr3 198022430 10529948 0.053175531680931296 0.318672551608918 chr4 191154276 10255206 0.05364884435020433 0.4049906305912396 chr5 180915260 8231151 0.04549727314323844 0.33022680084305656 chr6 171115067 8584105 0.050165687630534604 0.346446201579917 chr7 159138663 15551129 0.0977206211667117 1.6930779743092357 chr8 146364022 14823142 0.10127585862596752 0.5561804380166644 chr9 141213431 6386377 0.045224997047200136 0.6159277062247844 chr10 135534747 7915043 0.058398625999574856 0.8816893730140604 chr11 135006516 7613943 0.05639685568954316 0.4027118063353198 chr12 133851895 7839972 0.058571991080141224 0.34207812366627627 chr13 115169878 4342333 0.03770372145397254 0.2626476323342676 chr14 107349540 5100748 0.047515322375857406 0.347787609597423 chr15 102531392 4832169 0.047128678405146396 0.3003622562427037 chr16 90354753 4418468 0.04890133449869538 0.8362467867628041 chr17 81195210 4368537 0.0538028905892355 0.44230512516350423 chr18 78077248 3078434 0.039428054636351934 0.6942353986851556 chr19 59128983 3089278 0.052246425412052155 0.895395752613896 chr20 63025520 7227069 0.11466893093464361 0.517666405071631 chr21 48129895 2068617 0.04297987768309073 0.3340403238730614 chr22 51304566 1596806 0.03112405238941111 0.27550303594345543 chrMT 16571 370061 22.331844789089374 13.934730987165377 chrX 155270560 7092658 0.0456793483581176 0.3621674727677036 chrY 59373566 603448 0.010163580203351775 0.8734217386887014